Water in the Neck-Zipper Region of Kinesin

Neck linker （NL） is one of the most important mechanical elements of kinesin motors. The zipping up process of the neck-zipper （NZ） formed by NL and the related secondary structure elements is one of the major parts of kinesin＇s power stroke. All the weak interactions that are responsible for the formation of NZ are sensitive to or dependent on water. To investigate the role of water in the NZ region, a molecular dynamics （MD） model is set up with a crystal structure of kinesin 2KIN surrounded by a 10 A water layer, and minimization is performed to determine the positions of hydrogen atoms and other atoms. It is revealed that water molecules can assist the docking process of NL by forming hydrogen bonds at those positions where direct hydrogen bonding between the two sides of NZ is hindered and then acts as a constructive component of NZ at the docked state of NL. This result may improve the understanding of the mechanism for the docking of NL of kinesin wherein the function of water has not been comprehended sufficiently.     

Initial conformation of kinesin's neck linker

How ATP binding initiates the docking process of kinesin＇s neck linker is a key question in understanding kinesin mechanisms. By exploiting a molecular dynamics method, we investigate the initial conformation of kinesin＇s neck linker in its docking process. We find that, in the initial conformation, the neck linker has interactions with /30 and forms a ＇cover-neck bundle＇ structure with/30. From this initial structure, the formation of extra turns and the docking of the cover- neck bundle structure can be achieved. The motor head provides a forward force on the initial cover-neck bundle structure through ATP-induced rotation. This force, together with the hydrophobic interaction of ILE327 with the hydrophobic pocket on the motor head, drives the formation of the extra turn and initiates the neck linker docking process. Based on these findings, a pathway from ATP binding-induced motor head rotation to neck linker docking is proposed.     

Effects of Radius and Orientation of Single-Walled Carbon Nanotubes on Their Nonlinear Tensile Deformation Behaviour

By capturing the atomic information and reflecting the behaviour governed by a nonlinear potential function, an analytical molecular mechanics approach is applied to establish the constitutive relation for single-walled carbon nanotubes （SWCNTs）. The nonlinear tensile deformation curves of zigzag and armchair nanotubes with different radii are predicted, and the elastic properties of these SWCNTs are obtained. A conclusion is made that the nanotube radius has little effect on the mechanical behaviour of SWCNTs subject to simple tension, while the nanotube orientation has larger influence.     

Levitation and lateral forces between a point magnetic dipole and a superconducting sphere

The dipole–dipole interaction model is employed to investigate the angular dependence of the levitation and lateral forces acting on a small magnet in an anti-symmetric magnet/superconducting sphere system. Breaking the symmetry of the system enables us to study the lateral force which is important in the stability of the magnet above a superconducting sphere in the Meissner state. Under the assumption that the lateral displacement of the magnet is small compared to the physical dimensions of our proposed system, analytical expressions are obtained for the levitation and lateral forces as a function of the geometrical parameters of the superconductor as well as the height, the lateral displacement, and the orientation of the magnetic moment of the magnet. The dependence of the levitation force on the height of the levitating magnet is similar to that in the symmetric magnet/superconducting sphere system within the range of proposed lateral displacements. It is found that the levitation force is linearly dependent on the lateral displacement whereas the lateral force is independent of this displacement. A sinusoidal variation of both forces as a function of the polar and azimuthal angles specifying the orientation of the magnetic moment is observed. The relationship between the stability and the orientation of the magnetic moment is discussed for different orientations.     

Localized States of an Excess Electron in an Ionic Cluster

A theory of an electron affinity for an ionic cluster is proposed both in a quasiclassical approach and with quantization of a polarization electric field in a nanopartiele. A critical size of the cluster regarding in formation of an electron＇s autolocalized state, dependencies of energy and radius of a polaron on a cluster＇s size are obtained by a variational method. It has been found that binding energy of the electron in the cluster depends on a eluster＇s radius but a radius of electron＇s auto-localization does not depend on the cluster＇s radius and it equals to the polaron radius in a corresponding infinity crystal. A bound state of the electron in a cluster is possible only if the duster＇s radius is more than the polaron radius.     

Modified scaling angular spectrum method for numerical simulation in long-distance propagation

The angular method(AS)cannot be used in long-distance propagation because it produces severe numerical errors due to the sampling problem in the transfer function.Two ways can solve this problem in AS for long-distance propagation.One is zero-padding to make sure that the calculation window is wide enough,but it leads to a huge calculation burden.The other is a method called band-limited angular spectrum(BLAS),in which the transfer function is truncated and results in that the calculation accuracy decreases as the propagation distance increases.In this paper,a new method called modified scaling angular spectrum(MSAS)to solve the problem for long-distance propagation is proposed.A scaling factor is introduced in MSAS so that the sampling interval of the input plane can be adjusted arbitrarily unlike AS whose sampling interval is restricted by the detector’s pixel size.The sampling interval of the input plane is larger than the detector’s pixel size so the size of calculation window suitable for long-distance field propagation in the input plane is smaller than the size of the calculation window required by the zero-padding.Therefore,the method reduces the calculation redundancy and improves the calculation speed.The results from simulations and experiments show that MSAS has a good signal-to-noise ratio(SNR),and the calculation accuracy of MSAS is better than BLAS.     

Monte Carlo simulation on backward steps of single kinesin molecule

Kinesin is a stepping molecular motor travelling along the microtubule. It moves primarily in the plus end direction of the microtubule and occasionally in the minus-end, backward, direction. Recently, the backward steps of kinesin under different loads and temperatures start to attract interests, and the relations among them are revealed. This paper aims to theoretically understand these relations observed in experiments. After introducing a backward pathway into the previous model of the ATPase cycle of kinesin movement, the dependence of the backward movement on the load and the temperature is explored through Monte Carlo simulation. Our results agree well with previous experiments.     

Biased Diffusive Search Triggered by ATP Binding During Kinesin＇s Stepping

In this paper, we present an asymmetry conformational potential with a reflecting boundary and an absorbing boundary, in which the diffusive search of the free head of kinesin motor can be biased toward its forward binding site. Under a wide range of condition, using first-passage time analysis we perform numerical simulation to the Langevin equation, and obtain the dependence of the dwell time for forward steps on the load force. And we calculate the expression for the dwell time by the Laplace transform method. Both numerical and analytical results show that the dwell times exponentially depend on the load force, which provide a simple physical explanation for experimental data. Our results suggest that ATP binding-conformation change in the neck linker plays an important role in unidirectional steps during kinesin＇s mechanochemical cycle.     

Effect of surface tension on the mode selection of vertically excited surface waves in a circular cylindrical vessel

Singular perturbation theory of two-time-scale expansions was developed in inviscid fluids to investigate patternforming, structure of the single surface standing wave, and its evolution with time in a circular cylindrical vessel subject to a vertical oscillation. A nonlinear slowly varying complex amplitude equation, which involves a cubic nonlinear term,an external excitation and the influence of surface tension, was derived from the potential flow equation. Surface tensionwas introduced by the boundary condition of the free surface in an ideal and incompressible fluid. The results show that when forced frequency is low, the effect of surface tension on the mode selection of surface waves is not important.However, when the forced frequency is high, the surface tension cannot be neglected. This manifests that the function of surface tension is to cause the free surface to return to its equilibrium configuration. In addition, the effect of surface tension seems to make the theoretical results much closer to experimental results.     

Spin-Dependent Transport and Densities of States in Non-collinear Magnetic Barriers

The spin-dependent transport properties in the non-collinear pattern of series of δ-magnetic barriers are studied by using scattering theory and Green＇s function methods. The Green＇s function is obtained by using distorted wave approach and the scattering matrix is related by Fisher-Lee relationship. In addition to reproducing the results of Papp＇s and Xu＇s in parallel and antiparallel configurations, we also obtain further results, where arbitrary orientations of the magnetic barriers and arbitrary number of barriers are included. The main finding of our results is that the signs of polarizations can be switched around some ＂geometric unpolarized windows＂. The well-known antiparallel configuration has no such characteristics. Furthermore, we discuss spin-related partial densities of states in both polarized and unpolarized structures.     

Radiative Energy Shifts of an Atom Coupled to the Derivative of a Scalar Field near a Reflecting Boundary

We study the radiative energy level shifts of a two-level atom in dipole coupling to the derivative of a massless scalar quantum field in a spacetime with a perfectly reflecting boundary, and calculate the contributions of vacuum fluctuations and radiation reaction to the level shift. It is found that the energy level shift of the excited state is an oscillating function of the atom＇s distance from the boundary and it can either be positive or negative, while that of the ground state is always positive. The most remarkable feature is that the energy level shift of the ground state behaves like 1/z^4 when the atom＇s distance from the boundary, z, is very large as compared to the transition wavelength of the atom, while it behaves like 1/z^3 when z is very small     

Magnetic Properties of One-Dimensional Ferromagnetic Mixed-Spin Model within Tyablikov Decoupling Approximation

In this paper, we apply the two-time Green＇s function method, and provide a simple way to study the magnetic properties of one-dimensional spin-（S, s） Heisenberg ferromagnets. The magnetic susceptibility and correlation functions are obtained by using the Tyablikov decoupling approximation. Our results show that the magnetic susceptibility and correlation length are a monotonically decreasing function of temperature regardless of the mixed spins. It is found that in the case of S = s, our results of one-dimensional mixed-spin model is reduced to be those of the isotropic ferromagnetic Heisenberg chain in the whole temperature region. Our results for the susceptibility are in agreement with those obtained by other theoretical approaches.     

Finite-amplitude vibration of a bubble in water

The numerical results obtained by Rayleigh-Plesset （R-P） equation failed to agree with the experimental Mie scattering data of a bubble in water without inappropriately increasing the shear viscosity and decreasing the surface tension coefficient. In this paper, a new equation proposed by the present authors （Qian and Xiao） is solved. Numerical solutions obtained by using the symbolic computation program from both the R-P equation and the Qian-Xiao （Q-X） equation clearly demonstrate that Q-X equation yields best results matching the experimental data （in expansion phase）. The numerical solutions of R-P equation also demonstrate the oscillation of a bubble in water depends strongly upon the surface tension and the shear viscosity coefficients as well as the amplitude of driving pressure, so that the uniqueness of the numerical solutions may be suspected if they are varied arbitrarily in order to fit the experimental data. If the bubble＇s vibration accompanies an energy loss such as the light radiation during the contract phase, the mechanism of the energy loss has to be taken into account. We suggest that by use of the bubble＇s vibration to investigate the state equations of aqueous solutions seem to be possible. We also believe that if one uses this equation instead of R-P equation to deal with the relevant problems such as the ＇phase diagrams for sonoluminescing bubbles＇, etc., some different results may be expected.     

Resonance scattering of canonical elastic shells in absorbing fluid medium

Resonance scattering of elastic spherical shell and cylindrical shell while the surrounding fluid medium has absorption is studied. The normal mode solution derived using exact elastic theory and the separation of variables is still applicable. However, the scattering form function has to be modified for the absorbing medium, otherwise the unreasonable result would be obtained. The backscattering form function in the absorbing medium is redefined, and the form function of elastic spherical and cylindrical shell with vacuum or solid matter filled is calculated in various absorption conditions. The results show that the absorption of surrounding fluid leads to notable attenuation of the coincidence resonances in the mid-frequency, but it has a little influence on the low-frequency resonance scattering induced by the filler inside the shell.     

Relativistic Continuum Random Phase Approximation and Applications I. Formalism

A fully consistent relativistic continuum random phase approximation （RCRPA） is constructed in terms of the Green＇s function technique. In this method the contribution of the continuum spectrum to nuclear excitations is treated exactly by the single particle Green＇s function, which includes also the negative states in the Dirac sea in the no sea approximation. The theoretical formalism of RCRPA and numerical details are presented. The single particle Green＇s function is calculated numerically by a proper product of regular and irregular solutions of the Dirac equation. The numerical details and the formalism of RCRPA in the momentum representation are presented.     

Excitation spectrum and structure factor of a two-component Bose-Einstein condensate in different hyperfine states

The elementary excitation spectrum of a two-component Bose-Einstein condensate in different hyperfine states is obtained by Green＇s function method. It is found to have two branches. In the long wave-length limit, the two branches of the excitation spectrum are reduced to one phonon excitation and one single-particle excitation. The single-particle one has an energy gap. When the energy gap exists, we study the Landau critical velocity and the depletion of the condensate. With the obtained Green＇s functions, we calculate the structure factor of a two-component condensate. It is found that the static structure factor comprises only the branch of the phonon excitation and the single-particle excitation makes no contribution to the structure factor.     

A Novel Model of Interaural Time Difference Based on Spatial Fourier Analysis

Based on the spatial Fourier analysis, a statistical model of the individualized interaural time difference （ITD） is derived from the head-related transfer function database for a Chinese subject. The model reflects the spatial left-right symmetry and front-back asymmetry of lTD. Moreover, by using three anatomical parameters of head and pinna, the model is able to predict individualized ITD in the horizontal plane. Performance of the four subjects outside the database demonstrates that the mean of the total error is less than 20 μs, while the lateral performance is inferior to that at other directions.     

Prisoner's Dilemma Game on Two Types of Positively Correlated Networks

We study the effects of degree correlations on the evolution of cooperation in the prisoner＇s dilemma game with individuals located on two types of positively correlated networks. It is shown that the positive degree correlation can either promote or inhibit the emergence of cooperation depending on network configurations. Furthermore, we investigate the probability to cooperate as a function of connectivity degree, and find that high-degree individuals generally have a higher tendency to cooperate. Finally, it is found that small-degree individuals usually change their strategy more frequently, and such change is shown to be unfavourable to cooperation for both kinds of networks.     

COMPLETE EQUIVALENT CIRCUIT FOR RADIAL MODE OF PIEZOELECTRIC DISKS

Radial mode resonator of a piezoelectric disk is extensively applied to piezoelectric measure-ment;it has been a major subject of piezoelectric measurement in international standardization.Mason investigated this mode at first,and he derived the electrical admittance formula and approximateequivalent circuit that is only correct to the vicinity of the fundamental frequency.In this article,based on the admittance formula derived by Mason and using the Mittag-Leffler's theorem the completeequivalent circuit has been derived that is applicable to any frequency.It is proved that the completeequivalent circuit corresponds to the strict analytic solution derived from wave equation.     

A New Cooperation Mechanism of Kinesin Motors when Extracting Membrane Tube

Membrane tubes are important functional elements for riving cells. Experiments have found that membrane tubes can be extracted from giant lipid vesicles by groups of kinesin. How these motors cooperate in extracting the membrane tube is a very important issue but still unclear so far. In this paper, we propose a cooperation mechanism called two-track-dumbbell model, in which kinesin is regarded as a dumbbell with an end （tail domain） tethered on the fluid-like membrane and the other end （head domain） stepping on the microtubule. Taking account of the elasticity of kinesin molecule and the excluded volume effect of both the head domain and the tail domain of kinesin, which are not considered in previous models, we simulate the growth process of the membrane tube pulled by kinesin motors. Our results indicate that in the case of strong or moderate exclusion of motor tails, the average number of motors pulling the tube can be as high as 9 and thus motors moving along a single microtubule protofilament can generate enough force to extract membrane tubes from vesicles. This result is different from previous studies and may be tested by future experiments.